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Making alignments

Brian Foley btf at t10.lanl.gov
Fri Jan 16 17:29:04 EST 1998

James McInerney wrote:
> Jon,
> It is an absolute MUST to use the amino acid sequences
> for the purposes of alignment.  If you use DNA sequences there 
> is the prospect of introducing a single gap or two gaps, when 
> in all probability any indels that survived selective 
> purification would be multiples of three nucleotides (all 
> others would result in frameshift mutations which can be 
> very unusual customers).

	Well, if one sequence has a single-base insertion, 
relative to the other, the the DNA sequences could be more than 
99% identical and perfectly alignable, while the proteins
apear to be totally unrelated.  I prefer to align both the
DNA and the protein, and to use human intelligence to assess
the final alignment, prior to phylogenetic analysis.  Many
times the frameshifting mutations can be attributed to sequencing
error.  For example if one sequence is aggcaccccca and the other
is aggcacccca, it is quite easy to understand how the run of
C's could have been misread in one or the other of the
	Unfortunately, the same sites that are easy to mis-read
in sequencing are also places where DNA polymerases are likely
to make errors.  We cannot always assume the error is due to

	I like to align the DNA, then translate, then see if
I can adjust the gaps to have minimal impact on the protein
translation.  Then look carefully at frameshifting in/del sites 
that cannot be moved without lowering the aligmnet score.
I often ask authors to take another look at the raw sequence
data to see if a mis-read could have ocurred.

|Brian T. Foley               btf at t10.lanl.gov                       |
|HIV Database                 (505) 665-1970                         |
|Los Alamos National Lab      http://hiv-web.lanl.gov/index.html     |
|Los Alamos, NM 87544  U.S.A. http://www.t10.lanl.gov/~btf/home.html |

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